Key
Plots:
Summary plots - Sample strategy is on the y-axis and number of sites is on the x-axis. Each plot is paired by parameter level vertically and the values in the cells are the mean value across all of the simulations for that parameter level. Note that each average encompasses all of the other varying simulation parameters.
Full plots - Sample strategy is on the y-axis and number of sites is on the x-axis. Each plot represents a unique simulation and the values in the cells are the mean value across all of the 10 iterations of that simulation across all three unique landscape seeds (i.e., all three sets of Neutral Landscape Models) for a total of 30 replicates. For these plots: K = population size (not to be confused with the number of latent factors (K)), phi = selection strength, m = migration, H = spatial autocorrelation, r = correlation between environmental layers.
Methods:
K - number of latent factors used in LFMM
TPR - True Positive Rate
FDR - False Discovery Rate
lasso vs ridge- “lasso” and “ridge” are different methods utilized by LFMM that have different penalization functions (Caye et al., 2019)
pRDA - partial RDA conditioning on two PC axes to control for population genetic structure
Only results from the ridge method are used in the final models
TPR
| Linear mixed effect model | |||||||
|---|---|---|---|---|---|---|---|
| statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed) | |||||||
| Predictors | Fixed Effects | Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) |
| Sample number | 0.0002 | 2.7840 | 2.7840 | 1 | 15.3480K | 309.0550 | 1.6 × 10−68*** |
| Population size | 0.0260 | 2.5944 | 2.5944 | 1 | 15.3480K | 288.0033 | 5.2 × 10−64*** |
| Migration | 0.0529 | 10.7646 | 10.7646 | 1 | 15.3480K | 1194.9667 | 3.2 × 10−252*** |
| Selection strength | 0.0921 | 32.5538 | 32.5538 | 1 | 15.3480K | 3613.7662 | 0.0*** |
| Spatial autocorrelation | 0.0950 | 34.6821 | 34.6821 | 1 | 15.3480K | 3850.0347 | 0.0*** |
| Environmental correlation | −0.0166 | 1.0521 | 1.0521 | 1 | 15.3480K | 116.7964 | 4.0 × 10−27*** |
| *** p < 0.001 | |||||||
| Tukey test | ||||
|---|---|---|---|---|
| pairwise ~ sampstrat | ||||
| Contrast | Estimate | SE | Z ratio | p |
| EG - G | −0.0008 | 0.0022 | −0.3907 | 0.9797586 |
| EG - R | 0.0028 | 0.0022 | 1.3075 | 0.5581221 |
| EG - T*** | 0.0143 | 0.0022 | 6.5824 | 2.8 × 10−10*** |
| G - R | 0.0037 | 0.0022 | 1.6982 | 0.3245660 |
| G - T*** | 0.0151 | 0.0022 | 6.9731 | 1.9 × 10−11*** |
| R - T*** | 0.0114 | 0.0022 | 5.2749 | 7.9 × 10−7*** |
| *** p < 0.001 | ||||
FDR
| Linear mixed effect model | |||||||
|---|---|---|---|---|---|---|---|
| statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed) | |||||||
| Predictors | Fixed Effects | Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) |
| Sample number | −0.0028 | 604.6185 | 604.6185 | 1 | 15.3480K | 4074.163713 | 0.0*** |
| Population size | 0.0091 | 0.3177 | 0.3177 | 1 | 15.3480K | 2.140991 | 0.140 |
| Migration | 0.0535 | 11.0042 | 11.0042 | 1 | 15.3480K | 74.150771 | 7.9 × 10−18*** |
| Selection strength | −0.0341 | 4.4620 | 4.4620 | 1 | 15.3480K | 30.066848 | 4.2 × 10−8*** |
| Spatial autocorrelation | 0.0813 | 25.3925 | 25.3925 | 1 | 15.3480K | 171.105060 | 6.9 × 10−39*** |
| Environmental correlation | −0.0109 | 0.4526 | 0.4526 | 1 | 15.3480K | 3.049905 | 0.081 |
| *** p < 0.001 | |||||||
| Tukey test | ||||
|---|---|---|---|---|
| pairwise ~ sampstrat | ||||
| Contrast | Estimate | SE | Z ratio | p |
| EG - G | 0.0097 | 0.0088 | 1.1006 | 0.68917026 |
| EG - R | −0.0193 | 0.0088 | −2.1984 | 0.12363814 |
| EG - T*** | −0.0435 | 0.0088 | −4.9431 | 4.6 × 10−6*** |
| G - R** | −0.0290 | 0.0088 | −3.2989 | 5.4 × 10−3** |
| G - T*** | −0.0531 | 0.0088 | −6.0437 | 9.0 × 10−9*** |
| R - T* | −0.0241 | 0.0088 | −2.7448 | 0.03081891* |
| *** p < 0.001 | ||||
| ** p < 0.01 | ||||
| * p < 0.05 | ||||
K
TPR
FDR
Total number of loci
Only results from the ridge method are used in the final models
TPR
| Linear mixed effect model | |||||||
|---|---|---|---|---|---|---|---|
| statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed) | |||||||
| Predictors | Fixed Effects | Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) |
| Sample number | −0.0010 | 1.4682 | 1.4682 | 1 | 34.5490K | 112.1134 | 3.7 × 10−26*** |
| Population size | 0.0223 | 4.2973 | 4.2973 | 1 | 34.5490K | 328.1426 | 5.3 × 10−73*** |
| Migration | 0.0375 | 12.1734 | 12.1734 | 1 | 34.5490K | 929.5717 | 1.7 × 10−201*** |
| Selection strength | 0.0757 | 49.5136 | 49.5136 | 1 | 34.5490K | 3780.8896 | 0.0*** |
| Spatial autocorrelation | 0.1029 | 91.4338 | 91.4338 | 1 | 34.5490K | 6981.9351 | 0.0*** |
| Environmental correlation | −0.0242 | 5.0647 | 5.0647 | 1 | 34.5490K | 386.7470 | 1.2 × 10−85*** |
| *** p < 0.001 | |||||||
| Tukey test | ||||
|---|---|---|---|---|
| pairwise ~ sampstrat | ||||
| Contrast | Estimate | SE | Z ratio | p |
| EG - EQ*** | 0.0098 | 0.0015 | 6.4694 | 3.0 × 10−10*** |
| EG - R*** | 0.0093 | 0.0015 | 6.1743 | 2.0 × 10−9*** |
| EQ - R | −0.0004 | 0.0015 | −0.2950 | 0.9531481 |
| *** p < 0.001 | ||||
FDR
| Linear mixed effect model | |||||||
|---|---|---|---|---|---|---|---|
| statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed) | |||||||
| Predictors | Fixed Effects | Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) |
| Sample number | 0.0090 | 119.4872 | 119.4872 | 1 | 34.5510K | 1.371798e+03 | 1.7 × 10−294*** |
| Population size | 0.0007 | 0.0043 | 0.0043 | 1 | 34.5510K | 4.942033e-02 | 0.820 |
| Migration | −0.0010 | 0.0095 | 0.0095 | 1 | 34.5510K | 1.086153e-01 | 0.740 |
| Selection strength | −0.0215 | 4.0100 | 4.0100 | 1 | 34.5510K | 4.603750e+01 | 1.2 × 10−11*** |
| Spatial autocorrelation | −0.0063 | 0.3439 | 0.3439 | 1 | 34.5510K | 3.948046e+00 | 0.047** |
| Environmental correlation | 0.0029 | 0.0707 | 0.0707 | 1 | 34.5510K | 8.115947e-01 | 0.370 |
| *** p < 0.001 | |||||||
| ** p < 0.05 | |||||||
| Tukey test | ||||
|---|---|---|---|---|
| pairwise ~ sampstrat | ||||
| Contrast | Estimate | SE | Z ratio | p |
| EG - EQ*** | 0.0124 | 0.0039 | 3.1771 | 4.2 × 10−3*** |
| EG - R | −0.0008 | 0.0039 | −0.1998 | 0.9782368 |
| EQ - R*** | −0.0131 | 0.0039 | −3.3769 | 2.1 × 10−3*** |
| *** p < 0.01 | ||||
K
TPR
FDR
Total number of loci
To determine the effect of K-selection on performance we ran LFMM using a constant K for all of the subsampled datasets from the same simulation (i.e., all sample sizes and strategies had the same K) and compared that to K-selection based on each sub-sampled dataset (i.e., K was allowed to vary by sample size and strategy). The constant K for each simulation was selected using a dataset of 1000 randomly selected individuals. For this test, we only evaluated the “ridge” and not the “lasso” method as our earlier tests demonstrated that, in general, the “ridge” method performed better. We compared the results using the same statistics (i.e., TPR and FDR) and linear mixed effects models. Overall, the final results did not vary substantially between constant and variable K and the effects of all the parameters tested remained the same.
TPR
| Linear mixed effect model | |||||||
|---|---|---|---|---|---|---|---|
| statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed) | |||||||
| Predictors | Fixed Effects | Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) |
| Sample number | 0.0002 | 2.5777 | 2.5777 | 1 | 15.3480K | 285.6968 | 1.6 × 10−63*** |
| Population size | 0.0267 | 2.7327 | 2.7327 | 1 | 15.3480K | 302.8711 | 3.4 × 10−67*** |
| Migration | 0.0530 | 10.7778 | 10.7778 | 1 | 15.3480K | 1194.5434 | 3.9 × 10−252*** |
| Selection strength | 0.0931 | 33.2480 | 33.2480 | 1 | 15.3480K | 3684.9903 | 0.0*** |
| Spatial autocorrelation | 0.0961 | 35.4706 | 35.4706 | 1 | 15.3480K | 3931.3324 | 0.0*** |
| Environmental correlation | −0.0166 | 1.0521 | 1.0521 | 1 | 15.3480K | 116.6116 | 4.4 × 10−27*** |
| *** p < 0.001 | |||||||
| Tukey test | ||||
|---|---|---|---|---|
| pairwise ~ sampstrat | ||||
| Contrast | Estimate | SE | Z ratio | p |
| EG - G | −0.0013 | 0.0022 | −0.6157 | 0.9271278 |
| EG - R | 0.0025 | 0.0022 | 1.1563 | 0.6545013 |
| EG - T*** | 0.0140 | 0.0022 | 6.4420 | 7.1 × 10−10*** |
| G - R | 0.0038 | 0.0022 | 1.7719 | 0.2869064 |
| G - T*** | 0.0153 | 0.0022 | 7.0577 | 1.0 × 10−11*** |
| R - T*** | 0.0115 | 0.0022 | 5.2858 | 7.5 × 10−7*** |
| *** p < 0.001 | ||||
FDR
| Linear mixed effect model | |||||||
|---|---|---|---|---|---|---|---|
| statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed) | |||||||
| Predictors | Fixed Effects | Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) |
| Sample number | −0.0029 | 646.8019 | 646.8019 | 1 | 15.3480K | 4374.882787 | 0.0*** |
| Population size | 0.0140 | 0.7517 | 0.7517 | 1 | 15.3480K | 5.084648 | 0.024** |
| Migration | 0.0547 | 11.4783 | 11.4783 | 1 | 15.3480K | 77.637772 | 1.4 × 10−18*** |
| Selection strength | −0.0357 | 4.8980 | 4.8980 | 1 | 15.3480K | 33.129151 | 8.8 × 10−9*** |
| Spatial autocorrelation | 0.0770 | 22.7504 | 22.7504 | 1 | 15.3480K | 153.880959 | 3.6 × 10−35*** |
| Environmental correlation | −0.0088 | 0.2972 | 0.2972 | 1 | 15.3480K | 2.009990 | 0.160 |
| *** p < 0.001 | |||||||
| ** p < 0.05 | |||||||
| Tukey test | ||||
|---|---|---|---|---|
| pairwise ~ sampstrat | ||||
| Contrast | Estimate | SE | Z ratio | p |
| EG - G | 0.0068 | 0.0088 | 0.7754 | 0.86563528 |
| EG - R | −0.0184 | 0.0088 | −2.0991 | 0.15333943 |
| EG - T*** | −0.0424 | 0.0088 | −4.8354 | 7.9 × 10−6*** |
| G - R** | −0.0252 | 0.0088 | −2.8745 | 0.02109283** |
| G - T*** | −0.0492 | 0.0088 | −5.6108 | 1.2 × 10−7*** |
| R - T** | −0.0240 | 0.0088 | −2.7363 | 0.03156906** |
| *** p < 0.001 | ||||
| ** p < 0.05 | ||||
TPR
| Linear mixed effect model | |||||||
|---|---|---|---|---|---|---|---|
| statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed) | |||||||
| Predictors | Fixed Effects | Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) |
| Sample number | −0.0040 | 5.8037 | 5.8037 | 1 | 8.6290K | 552.7327 | 1.6 × 10−118*** |
| Population size | 0.0190 | 0.7830 | 0.7830 | 1 | 8.6290K | 74.5706 | 6.9 × 10−18*** |
| Migration | 0.0457 | 4.5032 | 4.5032 | 1 | 8.6290K | 428.8741 | 5.1 × 10−93*** |
| Selection strength | 0.0731 | 11.5391 | 11.5391 | 1 | 8.6290K | 1098.9616 | 6.1 × 10−227*** |
| Spatial autocorrelation | 0.1048 | 23.7248 | 23.7248 | 1 | 8.6290K | 2259.5020 | 0.0*** |
| Environmental correlation | −0.0252 | 1.3688 | 1.3688 | 1 | 8.6290K | 130.3630 | 5.6 × 10−30*** |
| *** p < 0.001 | |||||||
| Tukey test | ||||
|---|---|---|---|---|
| pairwise ~ sampstrat | ||||
| Contrast | Estimate | SE | Z ratio | p |
| EG - EQ | 0.0040 | 0.0027 | 1.4948 | 0.29338489 |
| EG - R*** | 0.0109 | 0.0027 | 4.0505 | 1.5 × 10−4*** |
| EQ - R** | 0.0069 | 0.0027 | 2.5556 | 0.02857052** |
| *** p < 0.001 | ||||
| ** p < 0.05 | ||||
FDR
| Linear mixed effect model | |||||||
|---|---|---|---|---|---|---|---|
| statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed) | |||||||
| Predictors | Fixed Effects | Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) |
| Sample number | −0.0073 | 19.7739 | 19.7739 | 1 | 8.6310K | 836.14415238 | 1.4 × 10−175*** |
| Population size | 0.0017 | 0.0065 | 0.0065 | 1 | 8.6310K | 0.27476374 | 0.60 |
| Migration | 0.0006 | 0.0007 | 0.0007 | 1 | 8.6310K | 0.02904367 | 0.86 |
| Selection strength | −0.0292 | 1.8461 | 1.8461 | 1 | 8.6310K | 78.06102539 | 1.2 × 10−18*** |
| Spatial autocorrelation | 0.0009 | 0.0016 | 0.0016 | 1 | 8.6310K | 0.06739987 | 0.80 |
| Environmental correlation | 0.0018 | 0.0071 | 0.0071 | 1 | 8.6310K | 0.29928678 | 0.58 |
| *** p < 0.001 | |||||||
| Tukey test | ||||
|---|---|---|---|---|
| pairwise ~ sampstrat | ||||
| Contrast | Estimate | SE | Z ratio | p |
| EG - EQ | 0.0006 | 0.0041 | 0.1489 | 0.9878524 |
| EG - R | −0.0017 | 0.0041 | −0.4238 | 0.9057716 |
| EQ - R | −0.0023 | 0.0041 | −0.5727 | 0.8347053 |
| Sampling | Population Genetics | Landscape | |||||
|---|---|---|---|---|---|---|---|
| Sampling type | Sample number | Population size | Migration | Selection strength | Spatial autocorrelation | Environmental correlation | |
| TPR | |||||||
| Constant K | individual | 0.0002 | 0.0267 | 0.0530 | 0.0931 | 0.0961 | −0.0166 |
| Variable K | individual | 0.0002 | 0.0260 | 0.0529 | 0.0921 | 0.0950 | −0.0166 |
| Constant K | site | −0.0040 | 0.0190 | 0.0457 | 0.0731 | 0.1048 | −0.0252 |
| Variable K | site | −0.0010 | 0.0223 | 0.0375 | 0.0757 | 0.1029 | −0.0242 |
| FDR | |||||||
| Constant K | individual | −0.0029 | 0.0140 | 0.0547 | −0.0357 | 0.0770 | n.s. |
| Variable K | individual | −0.0028 | n.s. | 0.0535 | −0.0341 | 0.0813 | n.s. |
| Constant K | site | −0.0073 | n.s. | n.s. | −0.0292 | n.s. | n.s. |
| Variable K | site | 0.0090 | n.s. | n.s. | −0.0215 | −0.0063 | n.s. |
Only results from the standard RDA (not the partial RDA) are used in the final models
TPR
| Linear mixed effect model | |||||||
|---|---|---|---|---|---|---|---|
| statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed) | |||||||
| Predictors | Fixed Effects | Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) |
| Sample number | 0.0002 | 2.8394 | 2.8394 | 1 | 15.3480K | 545.389450 | 1.5 × 10−118*** |
| Population size | 0.0165 | 1.0439 | 1.0439 | 1 | 15.3480K | 200.509665 | 3.1 × 10−45*** |
| Migration | 0.0438 | 7.3555 | 7.3555 | 1 | 15.3480K | 1412.856406 | 7.2 × 10−296*** |
| Selection strength | 0.0440 | 7.4213 | 7.4213 | 1 | 15.3480K | 1425.494641 | 2.2 × 10−298*** |
| Spatial autocorrelation | 0.0436 | 7.2900 | 7.2900 | 1 | 15.3480K | 1400.274445 | 2.3 × 10−293*** |
| Environmental correlation | 0.0036 | 0.0488 | 0.0488 | 1 | 15.3480K | 9.371404 | 2.2 × 10−3** |
| *** p < 0.001 | |||||||
| ** p < 0.01 | |||||||
| Tukey test | ||||
|---|---|---|---|---|
| pairwise ~ sampstrat | ||||
| Contrast | Estimate | SE | Z ratio | p |
| EG - G | 0.0005 | 0.0016 | 0.2768 | 0.9926010 |
| EG - R | 0.0029 | 0.0016 | 1.7594 | 0.2931233 |
| EG - T*** | 0.0110 | 0.0016 | 6.6817 | 1.4 × 10−10*** |
| G - R | 0.0024 | 0.0016 | 1.4826 | 0.4480091 |
| G - T*** | 0.0105 | 0.0016 | 6.4050 | 9.0 × 10−10*** |
| R - T*** | 0.0081 | 0.0016 | 4.9224 | 5.1 × 10−6*** |
| *** p < 0.001 | ||||
FDR
| Linear mixed effect model | |||||||
|---|---|---|---|---|---|---|---|
| statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed) | |||||||
| Predictors | Fixed Effects | Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) |
| Sample number | 0.0003 | 5.7961 | 5.7961 | 1 | 15.3480K | 373.26868 | 3.4 × 10−82*** |
| Population size | 0.0153 | 0.9004 | 0.9004 | 1 | 15.3480K | 57.98778 | 2.8 × 10−14*** |
| Migration | 0.0753 | 21.8007 | 21.8007 | 1 | 15.3480K | 1403.96987 | 4.2 × 10−294*** |
| Selection strength | 0.0647 | 16.0600 | 16.0600 | 1 | 15.3480K | 1034.26485 | 1.2 × 10−219*** |
| Spatial autocorrelation | 0.0610 | 14.2799 | 14.2799 | 1 | 15.3480K | 919.62815 | 3.1 × 10−196*** |
| Environmental correlation | 0.0091 | 0.3176 | 0.3176 | 1 | 15.3480K | 20.45101 | 6.2 × 10−6*** |
| *** p < 0.001 | |||||||
| Tukey test | ||||
|---|---|---|---|---|
| pairwise ~ sampstrat | ||||
| Contrast | Estimate | SE | Z ratio | p |
| EG - G | −0.0010 | 0.0028 | −0.3555 | 0.98460216 |
| EG - R | 0.0020 | 0.0028 | 0.6959 | 0.89870855 |
| EG - T*** | 0.0085 | 0.0028 | 2.9888 | 0.01487071*** |
| G - R | 0.0030 | 0.0028 | 1.0514 | 0.71907362 |
| G - T** | 0.0095 | 0.0028 | 3.3443 | 4.6 × 10−3** |
| R - T | 0.0065 | 0.0028 | 2.2929 | 0.09963697 |
| *** p < 0.05 | ||||
| ** p < 0.01 | ||||
TPR
FDR
Total number of loci
Only results from the standard RDA (not the partial RDA) are used in the final models
TPR
| Linear mixed effect model | |||||||
|---|---|---|---|---|---|---|---|
| statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed) | |||||||
| Predictors | Fixed Effects | Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) |
| Sample number | 0.0015 | 0.8335 | 0.8335 | 1 | 8.6290K | 232.154396 | 9.5 × 10−52*** |
| Population size | 0.0173 | 0.6489 | 0.6489 | 1 | 8.6290K | 180.732574 | 8.6 × 10−41*** |
| Migration | 0.0322 | 2.2403 | 2.2403 | 1 | 8.6290K | 623.983518 | 5.0 × 10−133*** |
| Selection strength | 0.0321 | 2.2322 | 2.2322 | 1 | 8.6290K | 621.743005 | 1.4 × 10−132*** |
| Spatial autocorrelation | 0.0315 | 2.1447 | 2.1447 | 1 | 8.6290K | 597.363316 | 1.3 × 10−127*** |
| Environmental correlation | 0.0019 | 0.0081 | 0.0081 | 1 | 8.6290K | 2.261166 | 0.13 |
| *** p < 0.001 | |||||||
| Tukey test | ||||
|---|---|---|---|---|
| pairwise ~ sampstrat | ||||
| Contrast | Estimate | SE | Z ratio | p |
| EG - EQ | −0.0001 | 0.0016 | −0.0550 | 0.9983351 |
| EG - R*** | 0.0076 | 0.0016 | 4.8378 | 3.9 × 10−6*** |
| EQ - R*** | 0.0077 | 0.0016 | 4.8928 | 3.0 × 10−6*** |
| *** p < 0.001 | ||||
FDR
| Linear mixed effect model | |||||||
|---|---|---|---|---|---|---|---|
| statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed) | |||||||
| Predictors | Fixed Effects | Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) |
| Sample number | 0.0018 | 1.1681 | 1.1681 | 1 | 8.6290K | 140.00975 | 4.7 × 10−32*** |
| Population size | 0.0133 | 0.3801 | 0.3801 | 1 | 8.6290K | 45.55864 | 1.6 × 10−11*** |
| Migration | 0.0378 | 3.0791 | 3.0791 | 1 | 8.6290K | 369.07182 | 1.4 × 10−80*** |
| Selection strength | 0.0336 | 2.4370 | 2.4370 | 1 | 8.6290K | 292.10683 | 2.0 × 10−64*** |
| Spatial autocorrelation | 0.0297 | 1.8994 | 1.8994 | 1 | 8.6290K | 227.67214 | 8.5 × 10−51*** |
| Environmental correlation | 0.0144 | 0.4449 | 0.4449 | 1 | 8.6290K | 53.32587 | 3.1 × 10−13*** |
| *** p < 0.001 | |||||||
| Tukey test | ||||
|---|---|---|---|---|
| pairwise ~ sampstrat | ||||
| Contrast | Estimate | SE | Z ratio | p |
| EG - EQ*** | 0.0057 | 0.0024 | 2.3728 | 0.04642683*** |
| EG - R** | 0.0085 | 0.0024 | 3.5382 | 1.2 × 10−3** |
| EQ - R | 0.0028 | 0.0024 | 1.1654 | 0.47395300 |
| *** p < 0.05 | ||||
| ** p < 0.01 | ||||
TPR
FDR
Total number of loci